package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JTable;
+import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
/**
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true));
+
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
fetchStructuresMetaData();
// revise filter options if no results were found
populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ discoverStructureViews();
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
discoverPDBStructuresThread.start();
}
+ private void discoverStructureViews()
+ {
+ if (Desktop.instance != null)
+ {
+ targetView.removeAllItems();
+ targetView.addItem(
+ new StructureViewer(ap.getStructureSelectionManager()));
+ if (lastTargetedView != null && !lastTargetedView.isVisible())
+ {
+ lastTargetedView = null;
+ }
+ int linkedViewsAt = 1;
+ for (StructureViewerBase view : Desktop.instance
+ .getStructureViewers(null, null))
+ {
+ StructureViewer viewHandler = (lastTargetedView != null
+ && lastTargetedView.sview == view) ? lastTargetedView
+ : StructureViewer.reconfigure(view);
+
+ if (view.isLinkedWith(ap))
+ {
+ targetView.insertItemAt(viewHandler,
+ linkedViewsAt++);
+ }
+ else
+ {
+ targetView.addItem(viewHandler);
+ }
+ }
+ targetView.setVisible(targetView.getItemCount() > 1);
+
+ // finally, restore last targeted view by default.
+ if (lastTargetedView != null)
+ {
+ targetView.setSelectedItem(lastTargetedView);
+ }
+ }
+ }
+
+ private static StructureViewer lastTargetedView = null;
+
/**
* Updates the progress indicator with the specified message
*
}
- public void selectStructure(String...pdbids)
+ /**
+ * select structures for viewing by their PDB IDs
+ *
+ * @param pdbids
+ * @return true if structures were found and marked as selected
+ */
+ public boolean selectStructure(String... pdbids)
{
+ boolean found = false;
+
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
- : tbl_local_pdb;
+ : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
- if (currentView == VIEWS_FILTER)
+ if (restable == null)
{
-
- int pdbIdColIndex = restable.getColumn("PDB Id")
- .getModelIndex();
- for (int r = 0; r < restable.getRowCount(); r++)
+ // can't select (enter PDB ID, or load file - need to also select which
+ // sequence to associate with)
+ return false;
+ }
+
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+ for (int r = 0; r < restable.getRowCount(); r++)
+ {
+ for (int p = 0; p < pdbids.length; p++)
{
- for (int p=0;p<pdbids.length;p++)
- {
- if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
- .equalsIgnoreCase(pdbids[p]))
+ if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+ .equalsIgnoreCase(pdbids[p]))
{
- restable.setRowSelectionInterval(r, r);
- }
+ restable.setRowSelectionInterval(r, r);
+ found = true;
}
}
}
+ return found;
}
/**
* Handles action event for btn_ok
@Override
public void ok_ActionPerformed()
{
+ showStructures(false);
+ }
+
+ /**
+ * structure viewer opened by this dialog, or null
+ */
+ private StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
- new Thread(new Runnable()
+ Runnable viewStruc = new Runnable()
{
@Override
public void run()
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[]
{ selectedSequence });
}
DataSourceType.FILE, selectedSequence, true,
Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ sViewer = launchStructureViewer(
+ ssm, new PDBEntry[]
+ { fileEntry }, ap,
new SequenceI[]
{ selectedSequence });
}
- closeAction(preferredHeight);
- mainFrame.dispose();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
+ }
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
+ {
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
+ {
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
+ {
+
+ }
}
- }).start();
+ }
}
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
return foundEntry;
}
- private void launchStructureViewer(StructureSelectionManager ssm,
+ /**
+ * @param ssm
+ * @return targetted structure view (new or existing) configured according to
+ * superpose checkbox
+ */
+ public StructureViewer getTargetedStructureViewer(
+ StructureSelectionManager ssm)
+ {
+ Object _sv = targetView.getSelectedItem();
+ StructureViewer sv;
+ if (_sv == null)
+ {
+ sv = new StructureViewer(ssm);
+ } else {
+ sv = (StructureViewer) _sv;
+ }
+ sv.setSuperpose(chk_superpose.isSelected());
+ return sv;
+ }
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm,
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
long progressId = sequences.hashCode();
setProgressBar(MessageManager
.getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer sViewer = new StructureViewer(ssm);
- setProgressBar(null, progressId);
+ final StructureViewer sViewer = getTargetedStructureViewer(ssm);
+ sViewer.setSuperpose(chk_superpose.isSelected());
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
setProgressBar(null, progressId);
+ // remember the last viewer we used...
+ lastTargetedView = sViewer;
+ return sViewer;
}
/**
{
return progressBar.operationInProgress();
}
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
}
git://source.jalview.org / jalview.git / blobdiff